Arun Ahuja
Arun Ahuja
Most job on a full genome print the following warning: ``` Not enough space to cache broadcast_2 in memory! (computed 488.3 MB so far) ``` What is the broadcast variable...
- Upgrade to ADAM after https://github.com/bigdatagenomics/adam/pull/875 - Add back in test from https://github.com/hammerlab/guacamole/commit/564a7a4c3c8ee21ff3d56b7f9ec52bab4c875bcf - Update comment/functionality at thttps://github.com/hammerlab/guacamole/blob/master/src/main/scala/org/hammerlab/guacamole/pileup/PileupElement.scala#L132-L133
I wanted to discuss moving Guacamole back to a multi-module project. There are two main reasons I'd like to do this 1. Separate out Spark and non-Spark components, it'd be...
Currently `--reference-fasta gs://genomics-public-data/references/b37/Homo_sapiens_assembly19.fasta.gz` gives ``` Exception in thread "main" htsjdk.samtools.SAMException: Error opening file: Homo_sapiens_assembly19.fasta.gz at htsjdk.samtools.util.IOUtil.openGzipFileForReading(IOUtil.java:518) at htsjdk.samtools.util.IOUtil.openFileForReading(IOUtil.java:494) at htsjdk.samtools.reference.FastaSequenceFile.(FastaSequenceFile.java:53) ``` It is possible this failure is due to gzip,...
The variant caller in [High burden and pervasive positive selection of somatic mutations in normal human skin](http://www.ncbi.nlm.nih.gov/pubmed/25999502) uses the duplicates for evidence to support variants. We should examine how this...
Maybe out of scope for this project, but for TCGA data it would be useful to support PFS or OS being set to NaN. Right now, this gives an error...
At https://github.com/hammerlab/cohorts/blob/master/cohorts/load.py#L613-L619 - Is there a reason which catch this `IOError` and treat it the same as not having provided a VCF path? Any objections to removing that catch and...
Maybe we don't want this but perhaps a warning if I do `cohort.as_dataframe(join_with='non-existant data')`
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